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- PDB-7z0r: AtWRKY18 DNA-binding domain -

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Basic information

Entry
Database: PDB / ID: 7z0r
TitleAtWRKY18 DNA-binding domain
ComponentsWRKY transcription factor 18
KeywordsTRANSCRIPTION / transcription factor / DNA-binding domain / zinc binding
Function / homology
Function and homology information


regulation of defense response / response to salicylic acid / defense response to fungus / response to molecule of bacterial origin / sequence-specific DNA binding / defense response to bacterium / DNA-binding transcription factor activity / identical protein binding / nucleus
Similarity search - Function
WRKY transcription factor, plant / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain
Similarity search - Domain/homology
NITRATE ION / PHOSPHATE ION / WRKY transcription factor 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsGrzechowiak, M. / Jaskolski, M. / Ruszkowski, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science Centre Poland
CitationJournal: Int.J.Biol.Macromol. / Year: 2022
Title: New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain.
Authors: Grzechowiak, M. / Ruszkowska, A. / Sliwiak, J. / Urbanowicz, A. / Jaskolski, M. / Ruszkowski, M.
History
DepositionFeb 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: WRKY transcription factor 18
B: WRKY transcription factor 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7719
Polymers18,2082
Non-polymers5637
Water2,270126
1
A: WRKY transcription factor 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2323
Polymers9,1041
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: WRKY transcription factor 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5406
Polymers9,1041
Non-polymers4365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.576, 52.182, 81.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein WRKY transcription factor 18 / WRKY DNA-binding protein 18 / AtWRKY18


Mass: 9104.112 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: protein fragment encoding DNA-binding domain / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: WRKY18, At4g31800, F28M20.10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / Variant (production host): -GOLD / References: UniProt: Q9C5T4

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Non-polymers , 6 types, 133 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 0.1 M buffer system 3 (Tris (base); BICINE ) pH 8.5, 12.5% v/v MPD; 12.5% PEG 1000 and 12.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.66→40.52 Å / Num. obs: 18612 / % possible obs: 93.5 % / Redundancy: 12.7 % / Biso Wilson estimate: 15.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.071 / Net I/σ(I): 24.93
Reflection shellResolution: 1.66→1.76 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 5.68 / Num. unique obs: 2274 / CC1/2: 0.96 / % possible all: 73.4

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Processing

Software
NameVersionClassification
PHENIX1.18.1_3865refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2w1v

2w1v


Resolution: 1.66→40.52 Å / SU ML: 0.1459 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6449
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2188 919 5.01 %
Rwork0.178 17430 -
obs0.1801 18349 93.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.93 Å2
Refinement stepCycle: LAST / Resolution: 1.66→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1262 0 28 126 1416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111317
X-RAY DIFFRACTIONf_angle_d1.13781792
X-RAY DIFFRACTIONf_chiral_restr0.0619192
X-RAY DIFFRACTIONf_plane_restr0.0087233
X-RAY DIFFRACTIONf_dihedral_angle_d16.7789484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.740.237970.17941832X-RAY DIFFRACTION70.5
1.74-1.850.23051350.16872561X-RAY DIFFRACTION97.33
1.85-1.990.27261280.2092433X-RAY DIFFRACTION93.03
1.99-2.20.2241350.18362560X-RAY DIFFRACTION97.01
2.2-2.510.19271360.17982573X-RAY DIFFRACTION96.65
2.51-3.170.21421400.17552663X-RAY DIFFRACTION99.29
3.17-40.520.21381480.17062808X-RAY DIFFRACTION99.53
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.44594248299-1.028870020081.41209316491.039581527910.1772492998550.71962623218-0.0233741058959-0.063000584693-0.08064816954910.0137469644940.0200283968720.000385154884840.09111420105330.009761130594460.01216905231490.1453910621450.007371006858090.004826325814030.0902907868263-0.008445851033460.08913164555618.5478836602221.072508075338.9919839298
24.81338704253-0.560120242978-1.657509005864.277591380930.313413091342.96787106093-0.04427102218510.2822696167670.250466224045-0.1759355913350.0907699031213-0.437127404069-0.01383750400680.6100105231790.02900755393190.120416291953-0.00239916466688-0.002329681911760.233745821658-0.01293223173920.113858576829.8529555807717.830821376427.7284965916
36.32236370682-0.9282494954130.7730741481370.9728193759710.1045884717391.31855054306-0.01762676328760.1949862602680.00948153477236-0.00116027853401-0.007539393706520.032926177932-0.01635330394620.03650140283580.03463253479470.0988853022504-0.00805857025501-0.001770076170240.0479498345626-0.004854072175490.08300100277363.4887448289224.110393611334.3797951468
45.08600988604-0.4133704395931.024350267690.2198535062030.7275404566943.71519082532-0.235685610826-0.161434833557-0.8164217697510.2127942002640.136813358470.1757209479560.0512587741914-0.0799975403865-0.01357496164320.1524722919310.001566753286050.04872659915660.101972674515-0.009753710654670.18987465872610.063931004427.987703653545.7081573953
55.935393411425.322684378181.135935340575.940881819450.8985034163341.44540012425-0.1001474714440.199815368640.384629114726-0.2916028502270.04589947436210.160484367126-0.295885299994-0.1597643992660.05804006539320.1526284667330.0210145983203-0.005600124442110.0839353852110.006074185355860.1370966235332.5350368112337.329700572644.7162549829
63.105983965833.124644684532.419845134013.270922078792.716094211232.54900297838-0.252892543708-0.5488915401740.248355781361-0.33875972819-0.2296734807790.406621501093-0.421056636175-0.6505899710740.3904983539110.1126449613370.0442897849028-0.0317718641490.277748434792-0.02713096365640.126289453416-1.0256682154734.44780460855.9921064329
76.713326512252.997249775253.524119873382.934452270882.107397187734.068670382390.383178291466-0.541085237427-0.2565775064590.281095284925-0.339135357205-0.154235688388-0.0238205414683-0.0306962590506-0.04996272655810.150048779251-0.000736764268007-0.009852468233080.1578386434650.02666192192930.0893305834367.7855119998335.848827258557.3481736829
86.885945579713.58729401377-1.013541822144.61515175421-0.6836337535463.388569407210.1979660291-0.303094185178-0.1268297057830.220798264386-0.186371352143-0.0977342098303-0.05594289941-0.0198311401709-0.02026452677670.1132019903530.0227254149465-0.001519861718980.08105883115420.001478152529980.08945270491874.7697811821230.330486436450.9139412013
94.6506545632-1.523031715522.976541551250.617491065082-1.167861972312.19726709458-0.274908219596-0.640604587531-1.052057937490.07486847463090.2699332326160.228993944281-0.29855797896-0.2924658266530.02472588753810.299758884797-0.0049224013088-0.02928729300910.2057523003620.01402050849050.345058558008-13.212686477520.156054644549.9886863609
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 158 through 180 )AA158 - 1801 - 23
22chain 'A' and (resid 181 through 201 )AA181 - 20124 - 44
33chain 'A' and (resid 202 through 238 )AA202 - 23845 - 81
44chain 'B' and (resid 159 through 165 )BC159 - 1651 - 7
55chain 'B' and (resid 166 through 180 )BC166 - 1808 - 22
66chain 'B' and (resid 181 through 187 )BC181 - 18723 - 29
77chain 'B' and (resid 188 through 201 )BC188 - 20130 - 43
88chain 'B' and (resid 202 through 228 )BC202 - 22844 - 70
99chain 'B' and (resid 229 through 238 )BC229 - 23871 - 80

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